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Table 6 Gene set enrichment analysis (GSEA) of classifiers on their validation data

From: Discovery and validation of gene classifiers for endocrine-disrupting chemicals in zebrafish (danio rerio)

chemical

Brain GEP (F-ratio)

Brain classifiers enriched on brain GEP (FDR)

Ovary GEP (F-ratio)

Ovary classifiers enriched on ovary GEP (FDR)

Flutamide (FLU)

NA

NA

FLU-ovary (13.76)

VIN-ovary (0.174)

    

FLU-ovary(0.21)a;

    

KET-ovary (0.039)

    

PRO-ovary (0.123)

Prochloraz (PRO)

PRO-brain (24.75)

No enrichment

PRO-ovary (15.2)

PRO-ovary (0.067)

    

KET-ovary (0.163)

  1. Although the gene expression profiles (GEPs) were preprocessed as a whole by combining data from both brain and ovary, each GSEA was conducted by individual chemical-tissue conditions at a threshold of FDR ≤ 0.25. Classifiers enriched on the top or bottom of a ranked gene list are separated by a semicolon. If two classifiers for the same condition were both significant, only the most significant one is listed. Mapping of the probe IDs between the Agilent design 15064 and 19161 was based on identical probe sequences only. FDR, false discovery rate; F-ratio, maximum Fisher’s discriminant ratio. “NA”, a condition not included in the study.
  2. aWhen the GEPs were preprocessed with data from ovary only, the FDR for flutamide-ovary was 0.53.
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BMC Genomics

ISSN: 1471-2164

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